MuTect

Overview

MuTect is a Bayesian statistical framework for the sensitive and specific detection of somatic single-nucleotide variants (SNVs) in paired tumor/normal sequencing data. Developed at the Broad Institute, it uses a two-sample likelihood model to distinguish somatic mutations from germline variants and sequencing artifacts, with particular attention to low-allele-fraction variants in impure tumor samples. MuTect is widely applied in cancer exome and genome sequencing pipelines, typically paired with Indelocator for indel detection.

Used by

  • Applied alongside Indelocator, dRanger, BreakPointer, CLONET, ChainFinder, ABSOLUTE, and GISTIC v2 in WGS analysis of 57 prostate tumors; detected 356,136 somatic base-pair mutations across the cohort (mean 33 non-silent exonic per primary tumor) PMID:23622249
  • Used for somatic SNV calling in 149 esophageal adenocarcinoma WES pairs (and 16 WGS pairs) alongside Indelocator; median 104 non-silent coding mutations per tumor at median genome-wide frequency 9.9/Mb PMID:23525077
  • Used alongside SomaticSniper for somatic SNV calling in 60 ACC tumor/normal pairs (55 exome + 5 WGS, Illumina HiSeq 2000); yielded 710 validated nonsynonymous mutations across 643 genes PMID:23685749
  • Used to call somatic SNVs from whole-exome data of 45 BRAF V600 metastatic melanoma FFPE tumors (DeCOG cohort) aligned to hg19 via the Broad Picard/Firehose pipeline PMID:24265153.
  • Applied for somatic point-mutation calling in paired tumor/normal whole-exome sequencing of grade II glioma initial/recurrent pairs (n=23); mutation validation rate informed by independent re-genotyping PMID:24336570
  • Applied for somatic point-mutation calling on the Illumina HiSeq whole-exome arm (13 paired samples) of the rhabdomyosarcoma cohort (147 total tumor/normal pairs); combined with MutSig for significantly mutated gene identification PMID:24436047
  • Applied for somatic point-mutation calling on 130 TCGA bladder carcinoma WES tumor/normal pairs; identified mean 302 exonic mutations per sample and APOBEC TpC signature representing 51% of all mutations PMID:24476821
  • Used to call SNVs in pre-treatment urothelial carcinoma tumors (n=50), identifying ERCC2 mutations enriched in cisplatin responders. PMID:25096233
  • Used to call somatic SNVs in matched primary/metastasis CRC trios (n=69) as part of the MSK-IMPACT analysis pipeline. PMID:25164765
  • Used for somatic variant calling in MPNST WES discovery cohort (15 tumors) alongside other callers PMID:25240281
  • Used alongside VarScan 2.2.5 for somatic variant calling in 78 gastric adenocarcinoma WES samples; identified 13,866 total somatic mutations including 8,558 missense and 576 nonsense variants PMID:25583476
  • Used for somatic SNV and indel calling in the AA CRC WES pipeline (29 discovery tumor/normal pairs), contributing to identification of 20 significantly mutated genes in African American MSS CRC PMID:25583493
  • Used for somatic SNV and indel calling (with OxoG artifact filtering) on 29 lymph-node metastases from cSCC patients sequenced with DFCI-ONCOPANEL-1 (mean tumor coverage 82×); identified high UV mutation burden (~33 mut/Mb) and recurrent oncogenic alterations PMID:25589618
  • MuTect used for SNV calling in 109 microdissected PDA WES samples (≥14 tumor reads, ≥8 normal reads); 92% of 248 non-silent mutations validated by Sanger sequencing. PMID:25855536
  • MuTect used for somatic mutation calling in 150 mCRPC whole-exome samples (mean 160×/100× tumor/normal coverage). PMID:26000489
  • MuTect used for somatic SNV calling in whole-exome sequencing of adrenocortical carcinoma PMID:26095796
  • MuTect used for somatic SNV calling in MSK-IMPACT panel sequencing of pancreatic cancer PMID:26278805
  • MuTect used for somatic SNV calling in whole-exome and whole-genome sequencing of colorectal cancer PMID:26343386
  • Used for SNV calling alongside MutationSeq in whole-genome sequencing of 46 matched primary/recurrent medulloblastoma samples; contributed to identification of ~5-fold increased mutational burden at recurrence PMID:26760213.
  • One of four mutation callers (MuTect, Indelocator, VarScan, RADIA) used in ≥2-caller consensus strategy for somatic mutation detection across 820 TCGA diffuse glioma exomes PMID:26824661
  • MuTect used for somatic SNV detection in 114 metastatic CRPC biopsies (81 patients); confirmed TP53 and RB1 as top altered genes distinguishing CRPC-NE from CRPC-Adeno PMID:26855148
  • Used for somatic mutation calling in the discovery cohort of 6 plasmacytoid-variant bladder tumors profiled by whole-exome sequencing. PMID:26901067
  • Used for somatic mutation calling on WES data from 141 tumors (56 men) with metastatic CRPC (prad_fhcrc cohort); identified AR, TP53, RB1, and MSH2/MSH6 driver mutations across metastatic sites. PMID:26928463
  • Used for SNV calling in 619 CRC FFPE tumor/normal pairs alongside Indelocator (indels) and Strelka (concordant indel filtering) PMID:27149842
  • Used for somatic mutation calling in 1,144 NSCLC (660 ADC + 484 SqCC) tumor/normal exome pairs in the pan-lung landscape study PMID:27158780
  • Used (panel-of-normals filtering analogous to MuTect) for somatic mutation calling in 2,433 primary breast tumours from the METABRIC cohort targeted-sequencing study PMID:27161491
  • Used for SNV calling in 62 uRCC tumours profiled with the MSK-IMPACT 230-gene panel (matched normal available in 61/62 cases). PMID:27713405
  • SNV calling pipeline applied alongside SNVseeqer on 72 urothelial carcinoma WES samples; only ~28% of mutations were shared between matched pre/post-chemotherapy tumour pairs. PMID:27749842
  • Used (MuTect v1.1.7) as the primary substitution caller in analysis of 216 metastatic breast cancer whole-exome sequencing datasets, downstream of BWA-MEM alignment and GATK base recalibration PMID:28027327.
  • Used MuTect for somatic SNV calling from paired tumor-normal sequencing data PMID:28373299
  • Applied MuTect for somatic mutation calling from paired tumor-normal sequencing PMID:28445112
  • Used as one of three somatic variant callers (MuTect, Pindel, GATK somatic indel detector) in the MSK-IMPACT SNV/indel pipeline; all calls manually reviewed in IGV PMID:28481359
  • Applied for somatic SNV calling on CCA whole-genome and exome sequencing data in the ICGC cholangiocarcinoma cohort (489 tumors across three sequencing platforms) PMID:28667006
  • Used for somatic SNV calling (MuTect v1.1.4) in 1001 DLBCL whole-exome sequencing samples PMID:28985567
  • Used for SNV calling in 412 BLCA tumor-normal pairs identifying 128,772 SNVs; confirmed APOBEC-dominated mutational landscape (67% of SNVs) PMID:28988769
  • One of four somatic variant callers applied to 68 paired melanoma biopsies in the CA209-038 nivolumab trial; intersection of MuTect 1.1.4, SomaticSniper 1.0.4, VarScan 2.3.7, and Strelka 1.0.13 was used PMID:29033130
  • MuTect used for SNV calling in 35 metastatic CCRCC paired tumor/normal WES samples to identify PBRM1 LOF mutations enriched in anti-PD-1 responders PMID:29301960
  • MuTect used for SNV calling in 15 vulvar SCC paired tumor/normal WES samples (Korean cohort) aligned to hg19 with BWA v0.7.15 PMID:29422544
  • One of seven callers in the TCGA MC3 pipeline; detected the largest number of true positive SNVs and showed highest pair-wise agreement with MuSE; run by Broad Firehose PMID:29596782
  • Used to call SNVs (v1.1.6) across 1,013 prostate tumor/normal pairs in the prad_p1000 dataset, identifying 97 SMGs PMID:29610475

Notes

  • Requires matched tumor/normal BAM files; not designed for tumor-only mode in its original implementation.
  • Sensitivity is maintained down to ~5% variant allele fraction under typical WES coverage (80–100×).
  • All candidate variants are typically followed by validation with orthogonal methods (e.g., Sequenom, deep digital sequencing).

Sources

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